Author Archives: allenkarstens

University of Leeds’ study on early life on Earth

A group at The University of Leeds is working with a jet propulsion lab at NASSA to study some of the chemistry that could have possible led to the earliest life on earth. In the video on the link below he is talking about the chemistry of the vents at the bottom of the ocean that could have led to the production of this life! super cool.

“YEARS”, A song written by nature

So this guy had an awesome idea to design and create a type of record player that can read tree rings!

The actual sound is connected to what’s called a trigger. The trigger takes the frequency’s read by the scanner and play those same frequencies in a more familiar timbre. So in this case, it sounds like a piano!

There are some really interesting minor sounding harmonies in the areas of the tree where the rings show abuse. Check it out! Its pretty amazing.


The Debate!

So I watched to Bill Nye debate earlier this week. The topic was “Is creationism a viable model of creation in today’s modern Science?” The debate was really well moderated I thought and the questions selected from the audience were equally fair. But I watched this because I had never really taken the time to watch anything like this before so I was curious on how it worked.

I don’t really like the question or the aspect of “winning” a debate…. I like to see debates as formal, moderated discussions during which both sides gain an understanding of each others stance. Because I’m sure both of them will admit they learned form each other. Also along that note, very few people that take stances on this sort of topic are looking to possibly be persuaded. People tend to stick to their guns when it comes to religious controversy. So also that kind of takes away the “debating” i guess? Possibly in a sense.. So it really is just a heated discussion on which some people take score. Regardless, here’s one of the main things I took from it.

One of Nye’s high points was when he was asked “What came before the big-band?” Obviously he knew that would be brought up so he had an answer well rehearsed, but none the less a good answer. The answer reminded me of one of the first articles that Dr. Gibbon gave us during the wet lab, about constructive stupidity in science. Nye enthusiastically answered: (paraphrase) I don’t know! But  questions like that are what get me out of bed and to work every day. Its questions like that, that excite me and make me dig in and try to understand the question at hand! We have ideas! But nothing more, no proof.. Yet! Hopefully someone from Kentucky (Where the debate was being held) can some day answer that question for you!

So I thought that was a really good answer, he demonstrated he knew a lot of stuff earlier in his presentation (kinda sounded like a lecture at times, but I mean hey, its a scientific debate what do you expect??) but at the same time he showed that there’s just as much we don’t know as what we do know!

I would suggest if you have some free time to nerd out, to watch it! I enjoyed it and gave me several things to think about.

Bio Lab Take 2! Action!

Well its only the 3rd day of lab and its safe to say that the overwhelming feeling is scary familiar to the beginning of last semester! But even that in itself is comforting, after a few weeks in the wet lab I was very confident in what I was doing and that I was doing it right. But I am really excited to learn about this side of science. Its one thing to put a couple things in a test tube or a petri dish, but another to actually be performing this research and figuring out this mystery puzzle that i’m sure amigo is going to be. The element of uncertainty died down last semester after I switched to M-smeg, but now that we’re all back on arthrobacter I feel like i’m back in the real deal! So even after the crazy awesome concepts that we went over today, I’m ready to get into the groove of putting this puzzle together!

Th-th-th-that’s all folks! (Well for this semester)

So our last lab for this semester has come and gone. And making smores is an awesome tradition for the last day! And now that Bonesquad is shipped of and in the data banks, all that is left to do is to analyze the bands on the electrophoresis!
So I said in my last blog that I found a study in a Smithsonian magazine that was super cool so I thought I would summarize it for y’all. This was a study published in 2007 by Yale’s Infant Cognition Center. This study was attempt to tackle the question of wether or not humans are wired to know the difference between good and evil (or lesser good), or if the concept of good is like anything else, just a skill we pick up along the way.
The test was performed on 6 and 10 month old infants. A group of these kids were shown a puppet show which had this story line:
There was a bunny that was struggling to open a box. Then along came a bunny in a purple shirt. The bunny in the purple shirt held the box down and prevented the original bunny from opening the box. The next scene was similar. The same bunny was trying to open the box and another bunny came along in a green shirt and aided the original bunny and together they opened the box!
This scenario was played over several times for the kids to ensure that they understood what had happened. Then following the last showing of the play, they had a chance to meet the bunnies of the story! When they met the bunnies, both the bunny in the purple and green shirt offered each infant a cracker, but could only take one. While the magazine didn’t give exact percentages, they did say the kids “overwhelmingly” choose the cracker from the bunny in the green shirt.
While of course this offers no concrete evidence, (because what if the good bunny offered a cracker while the “bad” offered a cookie?) it does kind of point towards the idea that the knowledge of goods is something humans might be born with.


Today I finished my restriction digest. It was kind of stressful in the since that sometimes when pipetting .69 micro litters, its hard to tell if anything is actually being pipetted! (And not to mention the entertaining frenzy of everyone on that same step fighting for each of the enzymes and their perspective buffers!) But now that thats all done, i’m moving onto the final steps including the electrophoresis. This part of the lab has been so cool because i’ve gotten to work first hand with some unbelievable equipment for any undergraduate, especially for a freshman! (Heck, I even got to troubleshoot the photo spectrometer!) So I really am sad to see this experience go, but next semester is where we get to actually dive into our results and that too is exciting.

I remember when I first applied to this program. I was expecting to see some pretty cool stuff under a microscope and actually get some biology lab experience. But it really has turned out to be so much more. It still blows my mind with all the stuff that we’ve been able to do this semester! I want to believe Dr. Gibbon when he says that next semester is super cool, but I feel like comparing it to this semester is going to be pretty tough!


Oh, and I found a really really interesting study for my last blog post! So be on the lookout.

A day in the life…

Well not every day in research is worth bragging about.. yesterday was one of those days where not much got done and there wasn’t too much anyone could do about it. Yesterday I learned how to operate the spectrophotometer. While this is an amazing piece of equipment that at the end of the day did its job, it goes to show that sometimes things just don’t go as you planned. But! I did get my concentration for the DNA sample. I’m not sure if mine was really that concentrated, or if there is some contaminant DNA hiding somewhere in there.. but! I’ll be ready to calculate and perform my restriction digest on Wednesday!


So today was the coolest day of lab by far. I filtered my lycate from my 10 plate and then did both steps of the microscopy! Its absolutely insane that I’ve been able to be a part of this as a freshman. As soon as I got to band I told several people (upperclassmen) about it and some of them didn’t even know that Baylor even had an electron microscope! And ironically enough, the day I was super excited about my fancy bio lab it was “nerd day” for the band. (The last rehearsal of the week is always a spirit day and people dress up according to the theme) So while others wore suspenders and thick glasses, I just showed up and got to act like it! Even though it was far from acting.

But now that I think about it, I was in a rush to get to band and forgot to write all this in the lab notebook… looks like i’ll be stopping by tomorrow to do that!


Getting closer

So I feel like I’ve past that checkpoint. Now I’m done with my 10 plate web that I flooded on Monday and will collect the lycate. Wednesday I will start on the graphing for the microscope, and ill get to start working with the DNA of the phage.

So it makes sense why we all have to switch next semester to arthro for the sequencing of the phage, but it defiantly makes me wish I had tried just one more time to get that phage! But I still would be doing the same thing, so in the end theres no difference.

Its kind of funny when I talk to my parents from time to time, they will ask about the lab and earlier in the year I would be able to simplify it enough where they had the general idea of what I was working on. But now and especially the rest of the semester, its gotten pretty complicated for just a casual phone conversation! But I really feel like I have a firm grip on what i’m doing and what i’m going to do next!

I guess math occasionally has its interesting moments right?…

Well maybe not.. but regardless that was the story of today’s lab: Math. I carefully took my titer count and made my table for my webbing dilutions.

So I feel like in this lab, finding the phage is the obvious first checkpoint, and I feel like the next is getting your calculations and product of 10 webbed plates. So now that I’m getting closer to that second checkpoint, i’m getting excited!

New Discovery

So I was taking a break from studying and surfing the internet when I came across a really interesting article! A national geographic research team went to the top of Cape Melville, a mountain range in norther Australia that has been cut off from the rest of the world for centuries. While on this cliff they found 3 new species of animals, like obvious ones too! The picture below shows where in Australia they were searching and the 3 species they found. Nat Geo said that they will be sending another expedition there within the next several months to look for smaller species.



Not your average day in lab!

So I was expecting to just walk in and do my last plaque assay and be on my way last Wednesday.  So I walked in and found that there appeared to be more than one phage on my plates (still??) so I had to pick both the “halo’ed” and the “non-halo’ed” plaques and see if they are two different types! This meant I had to do 10 plates of plaque assays to get the question answered no big deal… yet. As I was diluting my samples and labeling my plates it seems that people were walking around and asking to borrow a bit more than normal, so came out of my world of pipetting to find that we were running out of TA, and pretty fast. So then after what feels like a longer story that it probably was, I ended up doing two streak tests and two plaque assays to account for our lack of TA. I stopped by the lab on Friday and it looks like the two plaques might be the same thing! So in the end at least I got to really learn how to do a streak test. But! i’m ready to move on and flood!

Keep on Keepin’ on!

After checking my first round of purification it was easy to see that the single type of plaque I picked was the VAST majority of the plaques found on my plate. Even on the first plaque assay it looked like the strength of the plaque was already there. The only thing I need to do is isolate and purify!

But now I have to be really careful that I pick the same type of plaque because the second most prominent plaque on the first assay was adopted! Which is really funny. I’ll get to see two of mine “grow up”!

Also on another note here was my first blog a that I didn’t post correctly so it didn’t show up on Bears in the SEA! Its a bit long but, I wrote about my experiences in the first few weeks of classes and my background in the sciences.




My high school had bio 1 for freshman, all other sciences classes were mostly chemistry/physics (and saying physics is pushing it). But our chemistry classes were insanely good. There were classes like marine biology and zoology… but those were taught by football coaches and compared to my Organic, inorganic, and AP chem classes, they might as well have been electives. But through the awesome chem teacher I had through all of those courses, I learned that chemistry can be pretty awesome. (Hints my bio-chem major! So far.)

So planning ahead is something I’m always doing, so with my dad having majored in biology (from Baylor!) and my mom in chemistry, they were the first ones to tell me bio-chem is crazy hard. Alright. So, if i’m going to pursue bio-chem I have to know I really like it. So I wasn’t sure how I was going to see that until I actually had a bio-chem course! (But honestly I wasn’t too worried, I mean its the first semester of freshman year..) Then came this class, I was probably most nervous about this class just because the main thing I remembered for Bio 1 was making a cell cake! (and the different organelles were different toppings.. it was fun.. and tasty..anyways..) So I knew bio was going to be my real first challenge of college. When the first few chapters kick in we were talking about basic chemistry I was relieved because that was my domain of knowledge! So off to a good start. Then lo-and-behold, the super super basics of bio chem come in! And honestly the first sign that I think told me i’m heading in the right direction is when were discussing (really anything) I know there’s another layer below it as far as what the actual changes in elements of the processes are doing! And that’s super cool! So, so far looks like bio-chem might be something I could put 25 hours a day studying if I really am interested in it! (Hahaha see what i did? I know there’s only 24 hours in a day.) But time, and much more knowledge, will tell!

So as far as the actual genomics lab goes, at first I felt the same way I did towards the bio class. I wasn’t really sure what I was getting myself into. But this past week I feel like was when the procedure and its purpose really clicked. While I knew what was going on earlier, now I feel like I could Email an old teacher about it and they would know what I was talking about! So i’m starting to really get into it a lot more now also because I truly understand what we’re trying to accomplish!

It’s Here!!

So my phage finally decided to show itself. While there’s a small part of me that really wanted to keep trying arthrobacter… I’m very glad to be moving on with the research! Now that i’ve done my first plaque assay, it looks like there are actually multiple types of phages in my one sample! ( I feel like the m-smeg is mocking me…) But certainly no complaints there! So its time for the purification process and getting this phage by itself!

An on another semi-biological note, on my home page there are always little grab-bag news stories, and they found this fish that can grew 18 feet long! Turns out this was an oarfish. They apparently only live in water that is thousands of feet deep, and are rarely seen dead or alive. (Insert Bon Jovi pun here.) The fish was found dead in the shallow waters around Catilina Island, which is of the coast of California. Not sure if this was just to make the Time article more interesting or if this is true but the article said that this is the fish believed to be behind many sea monster stories! So the fish was buried and the marine biologists who found it are waiting for it to naturally decompose before retrieving its skeleton. (I watched the video of it and the lady who found it was wearing a Texas A&M shirt… So lets be honest, this is cool, but not that cool.)